Align Glyoxylate reductase 1; EC 1.1.1.26 (characterized)
to candidate 6936424 Sama_0612 D-lactate dehydrogenase (RefSeq)
Query= SwissProt::P53839 (350 letters) >FitnessBrowser__SB2B:6936424 Length = 329 Score = 115 bits (287), Expect = 2e-30 Identities = 67/196 (34%), Positives = 108/196 (55%), Gaps = 6/196 (3%) Query: 91 AGYDQIDVEPFKKRHIQVANVPDLVSNATADTHVFLLLGALRNFGIGNRRLIEGNWPEAG 150 AG++ +D+E K + V NVP + A+ V L+L R +R + N+ G Sbjct: 77 AGFNNVDLEEAKHLGMTVVNVPAYSPESVAEHTVALMLTLNRKIHKAYQRTRDANFSLEG 136 Query: 151 PACGSPFGYDPEGKTVGILGLGRIGRCILERLKPFGFENFIYHNRHQLPSEEEHGCEYVG 210 G++ GKTVG++G G+IG + L FG + + + P+ E G Y+ Sbjct: 137 LV-----GFNMHGKTVGVIGTGKIGLATIRILLGFGCK-VVAFDPFPSPAVEALGVPYLE 190 Query: 211 FEEFLKRSDIVSVNVPLNHNTHHLINAETIEKMKDGVVIVNTARGAVIDEQAMTDALRSG 270 +E LK D+VS++ PL HHL+ AET KMK GV+++NT+RG +++ +AL+ G Sbjct: 191 LDELLKLCDVVSLHCPLTKENHHLLRAETFAKMKPGVMVINTSRGGLLNAFDAMEALKVG 250 Query: 271 KIRSAGLDVFEYEPKI 286 +I + GLDV+E E ++ Sbjct: 251 QIGALGLDVYENEKEL 266 Lambda K H 0.317 0.136 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 247 Number of extensions: 9 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 350 Length of database: 329 Length adjustment: 28 Effective length of query: 322 Effective length of database: 301 Effective search space: 96922 Effective search space used: 96922 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory